diff --git a/.travis.yml b/.travis.yml
index 966b7d7bac4..70132e46ffd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -47,9 +47,7 @@ matrix:
 script:
   - |
     if [ -z ${INTEGRATION} ]; then
-      cargo build
-      cargo test
-      cargo test -- --ignored
+      cargo build && cargo test && cargo test -- --ignored
     else
       ./ci/integration.sh
     fi
diff --git a/Cargo.lock b/Cargo.lock
index 5ed591d42be..40979a53bd6 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -24,6 +24,14 @@ dependencies = [
  "winapi 0.3.8 (registry+https://github.com/rust-lang/crates.io-index)",
 ]
 
+[[package]]
+name = "ansi_term"
+version = "0.12.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+dependencies = [
+ "winapi 0.3.8 (registry+https://github.com/rust-lang/crates.io-index)",
+]
+
 [[package]]
 name = "arrayref"
 version = "0.3.5"
@@ -794,6 +802,7 @@ name = "rustfmt-nightly"
 version = "1.4.10"
 dependencies = [
  "annotate-snippets 0.6.1 (registry+https://github.com/rust-lang/crates.io-index)",
+ "ansi_term 0.12.1 (registry+https://github.com/rust-lang/crates.io-index)",
  "bytecount 0.6.0 (registry+https://github.com/rust-lang/crates.io-index)",
  "cargo_metadata 0.8.2 (registry+https://github.com/rust-lang/crates.io-index)",
  "derive-new 0.5.8 (registry+https://github.com/rust-lang/crates.io-index)",
@@ -1085,6 +1094,7 @@ dependencies = [
 "checksum aho-corasick 0.7.6 (registry+https://github.com/rust-lang/crates.io-index)" = "58fb5e95d83b38284460a5fda7d6470aa0b8844d283a0b614b8535e880800d2d"
 "checksum annotate-snippets 0.6.1 (registry+https://github.com/rust-lang/crates.io-index)" = "c7021ce4924a3f25f802b2cccd1af585e39ea1a363a1aa2e72afe54b67a3a7a7"
 "checksum ansi_term 0.11.0 (registry+https://github.com/rust-lang/crates.io-index)" = "ee49baf6cb617b853aa8d93bf420db2383fab46d314482ca2803b40d5fde979b"
+"checksum ansi_term 0.12.1 (registry+https://github.com/rust-lang/crates.io-index)" = "d52a9bb7ec0cf484c551830a7ce27bd20d67eac647e1befb56b0be4ee39a55d2"
 "checksum arrayref 0.3.5 (registry+https://github.com/rust-lang/crates.io-index)" = "0d382e583f07208808f6b1249e60848879ba3543f57c32277bf52d69c2f0f0ee"
 "checksum arrayvec 0.4.12 (registry+https://github.com/rust-lang/crates.io-index)" = "cd9fd44efafa8690358b7408d253adf110036b88f55672a933f01d616ad9b1b9"
 "checksum atty 0.2.13 (registry+https://github.com/rust-lang/crates.io-index)" = "1803c647a3ec87095e7ae7acfca019e98de5ec9a7d01343f611cf3152ed71a90"
diff --git a/Cargo.toml b/Cargo.toml
index 89cd280062b..351486b0a78 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -57,6 +57,7 @@ annotate-snippets = { version = "0.6", features = ["ansi_term"] }
 structopt = "0.3"
 rustfmt-config_proc_macro = { version = "0.2", path = "config_proc_macro" }
 lazy_static = "1.0.0"
+ansi_term = "0.12"
 
 # A noop dependency that changes in the Rust repository, it's a bit of a hack.
 # See the `src/tools/rustc-workspace-hack/README.md` file in `rust-lang/rust`
diff --git a/Configurations.md b/Configurations.md
index e1885aba836..0064f561720 100644
--- a/Configurations.md
+++ b/Configurations.md
@@ -1881,7 +1881,7 @@ specific version of rustfmt is used in your CI, use this option.
 - **Possible values**: any published version (e.g. `"0.3.8"`)
 - **Stable**: No (tracking issue: #3386)
 
-## `skip_children`
+## `skip_children` (DEPRECATED #3587)
 
 Don't reformat out of line modules
 
diff --git a/src/bin/main.rs b/src/bin/main.rs
index 661502a2e0e..ccbfb4052e2 100644
--- a/src/bin/main.rs
+++ b/src/bin/main.rs
@@ -11,6 +11,8 @@ use std::io::{self, stdout, Read, Write};
 use std::path::{Path, PathBuf};
 use std::str::FromStr;
 
+use ansi_term::Colour::Red;
+
 use getopts::{Matches, Options};
 
 use crate::rustfmt::{
@@ -513,6 +515,12 @@ struct GetOptsOptions {
     print_misformatted_file_names: bool,
 }
 
+fn deprecate_skip_children() {
+    let msg = "Option --skip-children is deprecated since it is now the default to not format \
+               submodules of given files (#3587)";
+    eprintln!("{}: {}", Red.bold().paint("Deprecation"), msg);
+}
+
 impl GetOptsOptions {
     pub fn from_matches(matches: &Matches) -> Result<GetOptsOptions, FailureError> {
         let mut options = GetOptsOptions::default();
@@ -529,6 +537,7 @@ impl GetOptsOptions {
 
             if options.unstable_features {
                 if matches.opt_present("skip-children") {
+                    deprecate_skip_children();
                     options.skip_children = Some(true);
                 }
                 if matches.opt_present("error-on-unformatted") {
@@ -540,6 +549,7 @@ impl GetOptsOptions {
             } else {
                 let mut unstable_options = vec![];
                 if matches.opt_present("skip-children") {
+                    deprecate_skip_children();
                     unstable_options.push("`--skip-children`");
                 }
                 if matches.opt_present("error-on-unformatted") {
diff --git a/src/config/config_type.rs b/src/config/config_type.rs
index 2eff7561392..b8f0691a7b9 100644
--- a/src/config/config_type.rs
+++ b/src/config/config_type.rs
@@ -58,6 +58,9 @@ macro_rules! create_config {
 
         use serde::{Deserialize, Serialize};
 
+        // for error messages
+        use ansi_term::Colour::Red;
+
         #[derive(Clone)]
         #[allow(unreachable_pub)]
         pub struct Config {
@@ -137,8 +140,17 @@ macro_rules! create_config {
             }
 
             fn fill_from_parsed_config(mut self, parsed: PartialConfig, dir: &Path) -> Config {
+                let deprecate_skip_children = || {
+                    let msg = "Option skip_children is deprecated since it is now the default to \
+                               not format submodules of given files (#3587)";
+                    eprintln!("{}: {}", Red.bold().paint("Deprecation"), msg);
+                };
+
             $(
                 if let Some(val) = parsed.$i {
+                    if stringify!($i) == "skip_children" {
+                        deprecate_skip_children()
+                    }
                     if self.$i.3 {
                         self.$i.1 = true;
                         self.$i.2 = val;